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  • Springer  (43,928)
  • Munksgaard International Publishers  (76)
  • 1990-1994  (44,004)
  • 1970-1974
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  • 1991  (44,004)
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  • 1
    Keywords: Leukemia / therapy ; Prognosis
    Notes: Last volumes with varying subtitle and editor.
    ISSN: 0949-7021
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  • 2
    Keywords: Hazardous Substances / toxicity
    Notes: Ceased with vol. 15(1999).
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Constructive approximation 7 (1991), S. 105-122 
    ISSN: 1432-0940
    Keywords: 41A15 ; 41A63 ; 46E20 ; 41A25 ; Bernoulli spline ; Periodic spline ; Reproducing kernel ; Spline interpolation ; Minimum norm interpolation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract Periodic spline interpolation in Euclidian spaceR d is studied using translates of multivariate Bernoulli splines introduced in [25]. The interpolating polynomial spline functions are characterized by a minimal norm property among all interpolants in a Hilbert space of Sobolev type. The results follow from a relation between multivariate Bernoulli splines and the reproducing kernel of this Hilbert space. They apply to scattered data interpolation as well as to interpolation on a uniform grid. For bivariate three-directional Bernoulli splines the approximation order of the interpolants on a refined uniform mesh is computed.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Constructive approximation 7 (1991), S. 161-194 
    ISSN: 1432-0940
    Keywords: 15A23 ; 14H99 ; 41A99 ; Descartes system ; Corner cutting ; Subdivision ; Total positivity ; Bernstein polynomials ; De Casteljau algorithm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract This paper demonstrates that Descartes Systems can be conveniently generated from matrix subdivision algorithms determined by totally positive matrices.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Constructive approximation 7 (1991), S. 149-160 
    ISSN: 1432-0940
    Keywords: 41A15 ; 41A05 ; 41A63 ; Closed surface ; Biquadratic B-spline ; Rectangular patch complex
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract In order to construct closed surfaces with continuous unit normal, this paper studies certain spaces of spline functions on meshes of four-sided faces. The functions restricted to the faces are biquadratic polynomials or, in certain special cases, bicubic polynomials. A basis is constructed of positive functions with “small” support which sum to 1 and reduce to tensor-product biquadratic B-splines away from certain “singular” vertices. It is also shown that the space is suitable for interpolating data at the midpoints of the faces.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Constructive approximation 7 (1991), S. 195-208 
    ISSN: 1432-0940
    Keywords: 41A05 ; 41A15 ; 65D07 ; Splines ; B-splines ; Knot insertion ; Subdivision ; Discrete B-splines ; Products of splines ; Degree raising of splines
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract In this paper it is shown how the algebraic product of two spline functions, each represented in terms of B-splines, can again be represented as a linear combination of suitable B-splines. As a corollary to this result we obtain an explicit representation of a given B-spline function in terms of B-splines of some arbitrary higher degree. This generalizes some known results for raising the degree by one. Recurrence relations for both products and degree raising are established that may be useful for computation.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Constructive approximation 7 (1991), S. 247-256 
    ISSN: 1432-0940
    Keywords: Primary 65D05 ; Secondary 41A15 ; Scattered data interpolation ; Multivariate approximation ; Surface fitting ; Minimum norm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract A generalization of G. M. Nielson's method for bivariate scattered data interpolation based upon a minimum norm network is presented. The essential part of the new method is the use of a variational principle for definition of function values as well as cross-boundary derivatives over the edges of a triangulation of the data points. We mainly discuss the case ofC 2 interpolants and present some examples including quality control with systems of isophotes.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Constructive approximation 7 (1991), S. 209-220 
    ISSN: 1432-0940
    Keywords: 41A15 ; 41A63 ; 65D07 ; Multivariate B-splines ; Simplex splines ; Cone splines ; Recurrence relations ; Multivariate divided differences
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract Some new results on multivariate simplex B-splines and their practical application are presented. New recurrence relations are derived based on [2] and [15]. Remarks on boundary conditions are given and an example of an application of bivariate quadratic simplex splines is presented. The application concerns the approximation of a surface which is constrained by a differential equation.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Constructive approximation 7 (1991), S. 221-246 
    ISSN: 1432-0940
    Keywords: 41A15 ; 41A10 ; 41A05 ; Bernstein-Bézier form ; C 1 surface ; G 1 surface ; Curve mesh interpolation ; (i, j, k)-match ; Vertex enclosure constraint ; Compatibility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract The interpolation of a mesh of curves by a smooth regularly parametrized surface with one polynomial piece per facet is studied. Not every mesh with a well-defined tangent plane at the mesh points has such an interpolant: the curvature of mesh curves emanating from mesh points with an even number of neighbors must satisfy an additional “vertex enclosure constraint.” The constraint is weaker than previous analyses in the literature suggest and thus leads to more efficient constructions. This is illustrated by an implemented algorithm for the local interpolation of a cubic curve mesh by a piecewise [bi]quarticC 1 surface. The scheme is based on an alternative sufficient constraint that forces the mesh curves to interpolate second-order data at the mesh points. Rational patches, singular parametrizations, and the splitting of patches are interpreted as techniques to enforce the vertex enclosure constraint.
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  • 10
    ISSN: 1432-0940
    Keywords: 41A15 ; Bézier patch ; Blossom ; de Boor algorithm ; B-patch ; B-spline ; de Casteljau algorithm ; Control point ; Knot insertion ; Knot net ; Polar form ; Symmetric algorithm ; Triangular patch
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract Using the concept of a symmetric recursive algorithm, we construct a new patch representation for bivariate polynomials: the B-patch. B-patches share many properties with B-spline segments: they are characterized by their control points and by a three-parameter family of knots. If the knots in each family coincide, we obtain the Bézier representation of a bivariate polynomial over a triangle. Therefore B-patches are a generalization of Bézier patches. B-patches have a de Boor-like evaluation algorithm, and, as in the case of B-spline curves, the control points of a B-patch can be expressed by simply inserting a sequence of knots into the corresponding polar form. In particular, this implies linear independence of the blending functions. B-patches can be joined smoothly and they have an algorithm for knot insertion that is completely similar to Boehm's algorithm for curves.
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  • 11
    ISSN: 1432-0940
    Keywords: 33A65 ; 34B20 ; Orthogonal polynomials ; Singular differential equation ; Legendre type boundary problem ; Weighted Sobolev space
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract The left-definite Legendre type boundary problem concerns the study of a fourth-order singular differential expressionM k [−] in a weighted Sobolev spaceH generated by a Dirichlet inner product. The fourth-order differential equation $$M_k [y] = \lambda y$$ has orthogonal polynomial eigenfunctions, called the Legendre type polynomials, associated with the eigenvalues $$\lambda _n = n(n + 1)(n^2 + n + 4\alpha - 2) + k.$$ In this paper, we show that the spaceC 2[−1, 1] is dense inH, from which it follows that the spectrum of the self-adjoint left-definite operatorS k [·] associated withM k [·] is a purely point spectrum and consists only of the eigenvaluesλ n . Comparisons betweenS k [·] and the associated right-definite operatorT k [·] are made. This work extends earlier work of Everitt, Krall, Littlejohn, and Williams.
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    Constructive approximation 7 (1991), S. 521-534 
    ISSN: 1432-0940
    Keywords: 33C20 ; 33C45 ; 30B70 ; 40A15 ; 39A10 ; Orthogonal polynomials ; Hypergeometric functions ; Contiguous relations ; Three term recurrence relations ; Jacobi matrix ; Spectral properties ; Dougall's theorem
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract From a contiguous relation obtained by Wilson for terminating 2-balanced very well-poised9 F 8 hypergeometric functions of unit argument, we derive a pair of three term recurrence relations for very well-poised7 F 6's. From these we obtain solutions to the recurrence relation for associated Wilson polynomials and spectral properties of the corresponding Jacobi matrix. A calculation of the basic weight function yields a generalization of Dougall's theorem.
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  • 13
    ISSN: 1432-0940
    Keywords: Primary 41A20 ; 41A21 ; Secondary 30E10 ; Multipoint Padé approximation ; Rational approximation ; Near-best approximation ; Best uniform approximation ; Interpolation ; Walsh array ; Distribution of poles
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract We show that the most of the time, most poles of diagonal multipoint Padé or best rational approximants to functions admitting fast rational approximation, leave the region of meromorphy. Following is a typical result: Letf be single-valued and analytic in CS, where cap(S)=0. Let {n j } j=1 ∞ be an increasing sequence of positive integers withn j+1/n j →1 asj→∞. Then there exists an infinite sequenceL of positive integers such that asj→∞,j∈L the total multiplicity of poles of any sequence of type (n j ,n j ) multipoint Padé or best rational approximants tof, iso(n j ) in any compactK in whichf is meromorphic. The sequenceL is independent of the particular sequence of multipoint Padé or best approximants, and yields the same behavior for “near-best” approximants. If the errors of best approximation on some compact set satisfy a weak regularity condition, then we may takeL={1,2,3,⋯}.
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  • 14
    ISSN: 1432-0975
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences
    Notes: Abstract Samples of solitary cryptofauna were collected from reef habitats before and after Hurricanes David and Frederic struck St. Croix, U.S.V.I. The intertidal beachrock zone suffered severe and sustained damage from waves, sand scouring and moving debris. Most bioeroded cavities in the substrate and several previously abundant cryptic taxa were completely obliterated from this environment for more than 6 months; numbers remained low or the pre-hurricane body size distribution had not been regained by the end of the 2 year study in a number of taxa. In 3 habitats at 2–3 m depths (fringing reef, patch reef, back of the bank barrier reef), some taxa underwent temporary decreases or dislocations, particularly on the fringing reef. Overall, however, this cryptofauna exhibited strong succession, with burrowers and then nestlers increasing above pre-hurricane densities. Many populations of nestlers were still increasing at the end of the 2 year study. Thus, the hurricanes enhanced densities of benthic invertebrates per piece of rubble (probably by providing fresh unburrowed substrate) in these moderately shallow subtidal habitats. On a deeper fore reef (12 m), we detected very few changes in cryptofaunal populations. The enhancement of invertebrate populations in reef habitats with intermediate levels of hurricane diturbance parallels recent findings that some species of corals have evolved colonizing life history tactics which allow them to prosper in moderately disturbed environments. Because the cryptofauna represent an important route of trophic flow (via predatory fishes) through the reef ecosystem, these relatively long term (≧2 y) changes in abundance of invertebrates have important implications for the structure and function of coral reef communities.
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  • 15
    ISSN: 1432-0975
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences
    Notes: Abstract A series of cold fronts passing over the western Arabian Gulf from December 1988 to March 1989 produced the longest period of sustained low water temperatures ever recorded in a coral reef area. Sea water temperatures recorded on two reefs during this period provide new estimates of lower thermal limits for reef coral survival. Severe mortality of the corals Acropora pharaonis and Platygyra daedalea occurred at the northern site where minimum temperatures fell below 11.5°C on four consecutive days and mean daily temperatures were 13°C or less for more than 30 days. However, Porites compressa, the principal reef-former in this area, and various faviid corals initially showed only sub-lethal effects and appeared normal after six months. Corals were not damaged at the southern site, where minimum water temperature fell below 12.5°C for two consecutive days, but mean temperatures were 14°C or less for only 5 non-consecutive days.
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  • 16
    ISSN: 1432-0983
    Keywords: Senescence ; Plasmid ; Neurospora ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Several field-collected strains of Neurospora crassa from the vicinity or Aarey, Bombay, India, are prone to precocious senescence and death. Analysis of one strain, Aarely-1e, demonstrated that the genetic determinants for the predisposition to senescence are maternally inherited. The senescence-prone strains contain a 7-kb, linear, mitochondrial DNA plasmid, maranhar, which is not present in long-lived isolates from the same geographical location. The maranhar plasmid has inverted terminal repeats with protein covalently bound at the 5′ termini. Molecular hybridization experiments have demonstrated no substantial DNA sequence homology between the plasmid and the normal mitochondrial (mtDNA) and nuclear genomes of long-lived strains of N. crassa. Integrated maranhar sequences were detected in the mtDNAs of two cultures derived from Aarey-1e, and mtDNAs with the insertion sequences accumulated during subculturing. Nucleotide sequence analysis of cloned fragments of the two insertion sequences demonstrates that that they are flanked by long inverted repeats of mtDNA. The senescence syndrome of the maranhar strains, and the mode of integration of the plasmid, are reminiscent of those seen in the kalilo strains of N. intermedia. Nonetheless, there is no detectable nucleotide sequence homology between the maranhar and kalilo plasmids.
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  • 17
    ISSN: 1432-0983
    Keywords: Mitochondria ; Introns ; Kluyveromyces
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have sequenced the intron in the large subunit ribosomal RNA gene from the mitochondrion of Kluyveromyces lactis. It is a typical group I intron but, unlike the corresponding intron (r1) in Saccharomyces cerevisiae, it does not contain an open reading frame. This intron is widespread in the genus Kluyveromyces although intron-less strains were also found in some species of this genus. Sequences homologous to the open reading frame of the S. cerevisiae ribosomal intron were detected in some strains of K. waltii, K thermotolerans and K. africanus.
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  • 18
    ISSN: 1432-0983
    Keywords: Mitochondria ; S. douglasii ; Intron ; TSL
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Mitochondrial genes coding for some components of the protein synthetic apparatus in S. douglasii have been studies in detail. A region containing stretches of high homology to the S. cerevisiae tRNA synthesis locus (TSL) and the tRNAfmet gene has been identified and sequenced. The organization of this region was very similar to that present in S. cerevisiae, including the presence of a possible transcription starting signal. The S. douglasii TSL gene is shorter due to several deletions which, however, do not involve the regions coding for RNA domains know to be required for the catalytic activity of mitochondrial RNAse P. The S. douglasii LSU rRNA gene has been shown to contain a typical group I intron highly homologous to its S. cerevisiae counterpart, except for the absence of the open reading frame which in S. cerevisiae codes for I-SceI endonuclease.
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  • 19
    ISSN: 1432-0983
    Keywords: Brassica napus ; CMS ; ‘Polima’ cytoplasm ; Mitochondrial transcription
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We report here on RFLP and Northern blot analyses of the ‘Polima’ CMS-System in Brassica napus. Mitochondrial (mt)DNA and plastid (pt)DNA data indicate that the restorer, as well as the sterile and restored plants, possess a pol cytoplasm but that the restores has no Brassica mt-plasmid. An additional substoichiometric 3.3 kb EcoRI ptDNA fragment is present in the restorer. The transcription patterns of 12 mitochondrial-encoded genes of the pol cytoplasm have been determined for male-sterile and restored plants. Transcription patterns of the atp6 gene are correlated with the nuclear background. Restorer and restored plants exhibit two additional transcripts not detectable in sterile plants.
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  • 20
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Pyrimidine salvage pathway ; Semi-dominant mutants ; FUR1 ; Uracil phosphoribosyl transferase ; Regulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In Saccharomyces cerevisiae, the protein encoded by the FUR1 gene is absolutely required for the expression of uracil phosphoribosyl transferase activity. The occurrence of semi-dominant mutations for 5-fluorouracil-(5FU)-resistance at this locus led us to clone and sequence the semi-dominant fur 1–5 allele. A single point mutation, resulting in the substitution of arginine 134 for serine, is responsible for this mutant phenotype. The fur 1–5 allele is transcribed and expressed at the same level as the wild-type allele. But, in contrast with the wild-type, the UPR Tase activity of the fur 1–5 mutant strain is stimulated in vitro by UTP and does not, therefore, correspond to a loss of feedback of UPR Tase activity. We found that uracil, as a free base, induces a significative increase in transcription and UPR Tase activity in a wild-type strain as well as in uracil-overproducing mutants which principally explains the high efficiency of the pyrimidine salvage pathway in S. cerevisiae.
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  • 21
    ISSN: 1432-0983
    Keywords: Cycloheximide resistance ; Plasmids ; Yeast Cloning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In CYH2/cyh2 heterozygous diploids of the yeast Saccharomyces cerevisiae resistance is dominant over sensitivity at low (0.5–5 μg/ml) cycloheximide (cyh) concentrations. The cyh-resistant haploid strain MMY1 confers relatively high (10 μg/ml) cyh-resistance to heterozygous diploids constructed by mating this strain with cyh-sensitive haploid strains. We present here a genetic and biochemical study of strain MMY1. Analysis of tetrads obtained from a MMY1 heterozygous diploid showed that two unlinked nuclear mutations, determining high-and low-cycloheximide resistance, were present in MMY1. From a genomic library of this strain, constructed in vector YCp50, two plasmids (pRC1 and pRC13) have been isolated which, respectively, confer high-and low-resistance phenotypes to cyh-sensitive S. cerevisiae strains. The restriction maps of pRC1 and pRC13 are totally unrelated. This finding suggests that the genes harboring the two mutations encoding cyh-resistance from MMY1 were cloned in plasmids pRC1 and pRC13, respectively. Pulse field gel electrophoresis showed that the DNA insert of pRC1 maps at either chromosome VII or XV, whereas that from pRC13 maps at chromosome XI. This latter gene appears to define a previously unreported locus and has been named cyh5. By restriction and nucleotide sequencing analysis, the cyh gene present in pRC1 has been shown to correspond to cyh2, which maps at chromosome VII. These results suggest that the dominant cyh-resistance phenotype conferred by MMY1 in heterozygous diploids is promoted by the presence of both cyh2 and cyh5. A 2.3 kb NcoI fragment, containing cyh2 from pRC1, has been inserted in vectors YCp50, YEp13 and YIp5. By selecting at discriminating cyh concentrations, the resulting constructs efficiently transform a variety of haploid and diploid yeasts of both laboratory and industrial origin.
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  • 22
    ISSN: 1432-0983
    Keywords: PET genes ; Yeast ; Mitochondria ; ATP synthase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary This study details the characteristics of two temperature-conditional pet mutants of yeast, strains ts1860 and ts379, which at the non-permissive temperature show deficiencies in the formation of three mitochondrially encoded subunits of the ATP synthase complex. By analysis of mitochondrial translation products, and of mitochondrial transcription in temperature shift experiments from the permissive (22°C) to the non-permissive (36°C) temperature, it was concluded that the nuclear mutations in both mutants primarily inhibit synthesis of ATP synthase subunit 9, and that reductions in subunit 8 and 6 synthesis are secondary pleiotropic effects. Following transfer to 36°C, cells of mutant ts379 display a near complete inhibition of subunit 9 synthesis within 1 h, coincident with a marked reduction in the level of the cognate oli1 mRNA. On the other hand, near complete inhibition of subunit 9 synthesis in strain ts1860 occurs after 3 h at 36°C, at which time there is little change in the level of subunit 9 mRNA. In both mutants the mRNA levels for subunits 6 and 8 are not significantly affected at the time of inhibition of subunit 9 synthesis. Provision of an alternative source of subunit 8, translated extra-mitochondrially for import into the organelle, does not overcome the mutant phenotype of either mutant at 36°C, confirming that subunit 8 is not the sole or primary deficiency in each mutant. The mutants indicate that the products of a least two nuclear genes (designated AEP1 and AEP2) are required for the expression of the mitochondrial oli1 gene and the synthesis of subunit 9. The product of the AEP1 gene (defective in mutant ts1860) is required for translation of oli1 mRNA while the AEP2 product (defective in mutant ts379) is essential either for the stability of oli1 mRNA or for the correct processing of precursor transcripts to the mature message.
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  • 23
    ISSN: 1432-0983
    Keywords: Trichoderma reesei ; Uridine auxotrophs ; Cloning ; Transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Uridine auxotrophs of the filamentous fungus Trichoderma reesei have been selected using a positive screening procedure with 5-fluoro orotate. Mutants deficient for the orotidine-5′-phosphate decarboxylase gene (ura3 mutants) and for the orotate phosphoribosyl transferase gene (ura5 mutants) have been characterized. The homologous ura3 and ura5 genes have been isolated and used to transform the auxotrophic mutants. Transformation efficiency with these homologous systems is very high (〉104 transformants per μg DNA). Transformation occurred by integration of vector DNA at homologous and ectopic loci. Mitotic instability was observed among some of the transformants. Sequence analysis at the protein level, of the T. reesei ura3 and ura5 genes showed extensive blocks of homology, with the corresponding genes from other organisms. The ura3 gene from T. reesei contains an insertion of 103 aa. A similar sequence is also found inserted in OMPdecase from the pyrenomycetes Neurospora crassa and Cephalosporium acremonium.
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  • 24
    ISSN: 1432-0983
    Keywords: Ribonuclease T2 ; Aspergillus oryzae ; Nucleotide sequence ; Transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Using synthetic oligonucleotide probes, we have cloned a genomic DNA sequence encoding a ribonuclease (RNase) T2 gene (rntB) from Aspergillus oryzae on a 4.8 kb HindIII fragment. DNA sequence analysis of the RNase T2 revealed the following: (1) The gene is arranged as five exons and four introns; (2) The deduced amino acid sequence contains 239 amino acid residues of the mature enzyme. In addition, there exist 17 amino acid residues thought to be a signal peptide sequence at the N-terminus and 20 amino acid residues at the C-terminus; (3) The nucleotide sequence of the rntB gene is homologous to those of the RNase Rh gene from Rhizopus niveus and the S2 stylar glycoprotein gene of Nicotiana alata with degree of about 51% and 47%, respectively; (4) A. oryzae and A. nidulans transformed with the cloned rntB gene had much higher ribonuclease T2 activity than wild-type strains.
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  • 25
    ISSN: 1432-0983
    Keywords: Achlya ambisexualis ; Heat shock ; hsp85 ; Steroid hormone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In Achlya ambisexualis, hsp85 is one of the characteristic mycelial heat shock proteins induced in response to a rapid elevation in temperature (Silver et al. 1983). This heat shock protein has the same electrophoretic mobility on two-dimensional gels and is antigenically related to an 85 kDa steroid hormone-regulated protein which constites a component of the putative Achlya steroid hormone-receptor complex. We report here the isolation of two distinct, yet highly related, hsp85 gene sequences from Achlya genomic libraries. Northern analyses, using these two Achlya genomic sequences as probes, suggest that there are two hsp85 message population in Achlya and that at least one of these is regulated by the steroid hormone antheridiol.
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  • 26
    ISSN: 1432-0983
    Keywords: Yeast ; Pichia inositovora ; Linear plasmids ; Killer toxin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Pichia inositovora, strain NRRL Y-18709, which contains three linear double-stranded DNA plasmids, pPinl-1, pPinl-2 and pPinl-3, was cured of these plasmids both by growing the strain in the presence of 50 μg/ml bisbenzimide, and by exposure to ultraviolet light. Both cured and uncured strains were tested for growth on a variety of carbon sources. No differences in growth response were detected, indicating no discernible involvement of the linear plasmids in the catabolism of these compounds. Culture supernatants of Pichia inositovora were shown to contain a substance larger than 100 kDa that is toxic to Saccharomyces cerevisiae, strain GS 1688. Toxin activity was optimal in YEPD assay plates containing 50 mM citrate buffer with a pH between 3.4 and 4.2. Culture supernatants from P. inositovora were also weakly active against Cephaloascus albidus, strain NRRL Y-18710, and Citeromyces matritensis, strain NRRL Y-18711. Concentrated supernatants from cured P. inositovora strains did not exhibit these activities, consistent with the hypothesis that this toxic activity is linear plasmid-encoded. Unlike the wellknown Kluyveromyces lactis system or the newly identified P. acaciae system, P. inositovora strains cured of their linear plasmids do not become detectably sensitive to toxin produced by the wild-type strain, suggesting a nonplasmid-encoded immunity function.
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  • 27
    ISSN: 1432-0983
    Keywords: Agaricus ; dsRNA ; Sequence ; Virus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary La France disease of the cultivated mushroom, Agaricus bisporus, is known to be associated with the presence of a number of dsRNA segments. The nucleotide sequences of the dsRNAs M2 (1.3 kb), M1 (1.55 kb) and L3 (2.8 kb), invariably associated with the disease, were determined. Putative coding sequences for proteins with molecular weights of 38, 40 and 87 kDa were found for M2, M1 and L3 dsRNAs, respectively. The average G+C content of these dsRNAs was 43%, close to that of A. bisporus nuclear DNA. The nucleotide sequences, as well as the amino acid sequences, appear to be unique, as no matching sequences could be found among databases. S3 dsRNA (0.39 kb), which is occasionally found in large amounts in diseased mushrooms, is an internally deleted variant of M2 dsRNA and is largely composed of the non-coding ends of that dsRNA.
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  • 28
    ISSN: 1432-0983
    Keywords: Ustilago ; Recombination ; Gene cloning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The REC1 gene of Ustilago maydis plays a key role in homologous recombination and the repair of damaged DNA. In order to understand the nature and functions of the gene product, the gene has been cloned by functional complementation. A 3.8 kb cloned fragment complements the pleiotropic mitotic phenotype of different rec1 alleles. It does not complement the UV sensitivity of two other sensitive mutants. Disruption of the chromosomal copy of the 1.566 kb open reading frame within this fragment reproduces the rec1 pleiotropic phenotype. Furthermore, in diploids this disrupted reading frame is unable to complement previously characterised rec1 alleles.
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  • 29
    ISSN: 1432-0983
    Keywords: Schizosaccharomyces pombe ; ste gene ; Conjugation ; Mating pheromones
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Mutants which carry a leaky UGA nonsense mutation in the fertility gene ste10 are characterized by a deformed cell morphology which resembles that described in the literature for sterile ras1 - (ste5) and ral1 to ral4 mutant cells. Although frequent conjugation attempts are observed in combinations of two ste10 mutant strains of opposite heterothallic mating type, zygotes and asci are formed only rarely and the fertility of such crosses remains low (not more than 1% of the fertility of comparable crosses of two ste + wild-type strains). The fertility is considerably increased, however, in combinations of the ste10 mutant with ste + wild-type strains (up to 10% if the h − partner, and more than 30% if the h + partner, carries the ste10 mutation).
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  • 30
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    Electronic Resource
    Springer
    Current genetics 20 (1991), S. 67-73 
    ISSN: 1432-0983
    Keywords: Schizosaccharomyces pombe ; ste genes ; Conjugation ; Meiosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Eight sterile mutants, which regain their fertility upon reactivation of an inactivated UGA suppressor allele of the serine tRNA gene sup3, are shown to carry UGA nonsense alleles of two established ste genes, ste1 (one mutant) and ste6 (two mutants), and of two novel genes, ste9 (four mutants) and ste10 (one leaky mutant of ras1 -/ste5-like cell morphology). The mutant alleles of ste1 and ste9 lead to a defect in both conjugation and meiosis, whereas those of ste6 and ste10 affect mating only. Two of the four genes map to chromosome I, ste1 in the left arm 6 cM distal of ura1, and ste9 in the right arm 3 cM distal of ade2. The ste10 and ste6 genes are located in the right arms of chromosomes II and III, respectively, the former 4 cM distal of trp1 and the latter 1 cM proximal or distal of trp3.
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  • 31
    ISSN: 1432-0983
    Keywords: AEP2 ; Yeast ; Mitochondria ; ATP synthase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The temperature-conditional pet mutant, ts379, of Saccharomyces cerevisiae fails to synthesize mitochondrial ATP synthase subunit 9 at the restrictive temperature due to mutation of a single nuclear locus, AEP2. The inability to synthesize subunit 9 correlates with a lowered accumulation of the cognate oli1 mRNA indicating that the AEP2 product is involved in oli1 transcript maturation or stabilization. The AEP2 gene has been isolated in this study from a wild-type yeast genomic library by genetic complementation of ts379 at the restrictive temperature. A 1740 nucleotide open-reading frame was observed that encodes a basic, hydrophilic protein of 67534 Da which possesses a putative mitochondrial address signal. Disruption of chromosomal DNA within this reading frame produced a non-conditional respiratory mutant unable to synthesize subunit 9, identifying the AEP2 gene. Hybridization analyses indicate that AEP2 is located on chromosome XIII and produces a 2.1 kb poly(A)+ transcript. Two additional open-reading frames were found in close proximity to that of AEP2. The three open-reading frames shared no significant homology with entries in several data bases.
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  • 32
    ISSN: 1432-0983
    Keywords: Schizosaccharomyces pombe ; Transcriptional regulation ; Thiamine ; nmt1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Wild-type fission yeast, growing in minimal medium, actively synthesizes thiamine and maintains an internal concentration which we have measured to be around 10 pmoles/107 cells. If thiamine is added to such cultures it is rapidly sequestered by the cell, and if added in excess (20μM) the internal concentration of thiamine rises almost 1000-fold to a maximum of around 9000 pmoles/107 cells before the transport mechanism is shut down. The kinetics of decay of intracellular thiamine to the basal level are consistent with simple dilution as the cell mass doubles. In parallel with this analysis, we have studied the transcriptional activity of the thiamine-sensitive gene nmt1 as a function of intracellular thiamine concentration. Transcription of this gene is rapidly repressed as the internal thiamine concentration rises and is only reactivated as the concentration falls to below about 50 pmoles/107 cells.
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  • 33
    ISSN: 1432-0983
    Keywords: Schizosaccharomyces pombe ; ste genes ; Mating pheromones ; Conjugation ; Meiosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Genetically heterothallic strains of various sterile mutants were assayed for residual production of the corresponding mating pheromone as well as responsivenes towards the opposite pheromone. No sexual activities were detected in ste11 strains (previously referred to as aff1 or steX, which we show are allelic), whilst the production of M factor was unaffected by ste1 to ste10 mutations. P factor production was still possible in class I ste mutants (ste5, ste6 and ste10), which also allow meiosis in diploid strains. With the exception of the leaky ste10-F23 mutant, no changes in cell morphology were induced by exposure to the opposite pheromone in the ste mutant strains.
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  • 34
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    Electronic Resource
    Springer
    Current genetics 20 (1991), S. 91-97 
    ISSN: 1432-0983
    Keywords: Pythium ; Mitochondrial plasmid ; RNA transcript
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Four circular plasmids, with a monomer size ranging from 3.2 to 4.94 kb, have been identified in isolates of P. aphanidermatum (two different plasmids), P. torulosum, and an unidentified echinulate isolate. The mitochondrial location has been confirmed for three of the plasmids. Each fungal isolate contained a single plasmid, present in both monomeric and oligomeric forms; plasmid monomers were present as open circles and as supercoiled forms. Restriction maps of the plasmids were dissimilar. Hybridization studies using cloned plasmids revealed no DNA sequence similarity among the different plasmids or between the plasmids and the nuclear or mitochondrial genome of the isolates from which they were recovered. Hybridization of labeled plasmid DNA to Northern transfers of mitochondrial RNA for two isolates indicate that what appears to be the predominant RNA transcript is unit length in size. For three isolates, the plasmid was retained following subculturing and was present in all asexual and sexual single-spore progeny evaluated. For one isolate of P. aphanidermatum the plasmid was unstable and was lost during subculturing.
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  • 35
    ISSN: 1432-0983
    Keywords: CBS1 protein ; Protein purification ; Mitochondrial presequence ; Protein sequencing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Yeast transformats harboring the CBS1 gene under the control of the strong ADC1 promoter on a high copy number plasmid express the mitochondrial CBS1 protein at artificially high levels. Over-expressed protein is imported into mitochondria and correctly processed to vield the mature mitochondrial 23.5 kDa form, but differs in its solubility properties from CBS1 in wild-type mitochondria. It forms insoluble protein aggregates, which are refractory to solubilization with 1% Taurodeoxycholate. We exploited this observation to separate CBS1 from the bulk of mitochondrial proteins and to isolate CBS1 after SDS gel electrophoresis. Determination of the amino-terminal amino acids of the purified protein reveals that the mature CBS1 protein starts with Ile30, at the characteristic distance of +2 amino acids from an arginine residue (Arg28). The cleavage site shows a remarkable homology to that of subunit 9 of the F0F1 ATPase from Neurospora crassa.
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  • 36
    ISSN: 1432-0983
    Keywords: Cytochrome c genes ; Candida glabrata ; Kluyveromyces lactis ; Transition to transversion ratios
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Base substitutions have been compared in two mitochondrial and two nuclear genes from three yeasts and three mammals. In yeasts, the two mitochondrial genes, cytochrome oxidase subunit 2 (COX2) and apocytochrome b (CYB), have fewer changes on a percentage basis than the nuclear-encoded cytochrome c (CYC) gene. By contrast, in mammals, the same mitochondrial genes have more mutations than CYC on a percentage basis. Sequence comparisons of the nuclear small-subunit ribosomal RNA (nSSU) gene shows that there are more substitutions per unit length in the three yeasts than in the three mammals. This result suggests that although the yeasts are more distantly related than the mammals, their mitochondrial genes have accumulated fewer changes.
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  • 37
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Bakers' and lager yeast ; Chromosomal and 2 μm DNA polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Seven strains of bakers' yeast were obtained as a representative sample of the Spanish baking industry. The nuclear genome was monitored for polymorphism by transverse alternating field electrophoresis (TAFE) and restriction maps of 2 μm DNA were produced. All seven strains were uniquely different when evaluated by their total chromosomal lengths whereas only two 2 μm variants were defined. There was no apparent correlation between chromosomal and plasmid polymorphism. The extensive chromosomal polymorphism within one 2 μm DNA type indicates the rapid and relatively recent evolution of the nuclear genome. The hybrid origin (S. cerevisiae-S.monacensis) of lager yeast was critically evaluated by TAFE analysis of S. cerevisiae and S. carlsbergensis chromosomes. The absence of corresponding S. cerevisiae chromosomes III and XIII in S. carlsbergensis argued against the hybrid origin of lager strains. We discuss limitations of the hybrid origin hypothesis of industrial yeasts and propose that the molecular coevolution observed in 2 μm DNA serves as a useful additional mechanism for rationalization of some of the structural polymorphism of the nuclear genome.
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  • 38
    ISSN: 1432-0983
    Keywords: Fission yeast ; cdc genes ; Cell division cycle ; Meiosis ; Sporulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Cell division cycle mutants defective in G1, DNA replication or nuclear division were tested for sporulation at semi-restrictive temperatures. In cdc1-7, cdc5-120, cdc17-L16 and cdc18-46 no abnormalities were observed; cdc10-129, cdc20-M10, cdc21-M6B, cdc23-M36 and cdc24-M38 formed four-spored asci but with a low efficiency; cdc22-M45 was completely defective in meiosis, but could conjugate and formed zygotes with a single nucleus. Mutants defective in the mitotic initiation genes cdc2, cdc25 and cdc13 were blocked in meiosis II. None of the wee1-50, adh.nim1 + and win1 + alleles had any affect on sporulation, suggesting that their interactions with cdc25 and cdc2 are specific to mitosis. The meiotic function of cdc13 is TBZ-sensitive and probably exerted downstream of cdc2. Single mutants in cut1 or cut2 did not effect sporulation, whereas the double mutant cut1 cut2 formed two-spored asci. The results demonstrate that the cell division cycle and the meiotic developmental pathway share common genes and regulatory cascades.
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  • 39
    ISSN: 1432-0983
    Keywords: Neurospora ; Cytochrome c oxidase ; COXII ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The maternally inherited [exn-5] mutant of Neurospora crassa is characterized by its slow-growth rate and deficiency of cytochrome aa 3 relative to wildtype strains. We have determined the DNA sequence of the COXI and COXII genes of the mutant, which encode subunits 1 and 2 of cytochrome c oxidase, respectively. No changes in the DNA sequence of the COXI gene relative to the corresponding wild-type gene were found. In the region of the COXII gene we found two alterations, one a C to T transition eight base pairs upstream of the coding sequence and the second within the coding sequence for subunit 2 affecting amino acid 27 of the precursor polypeptide (amino acid 15 of the mature polypeptide). The altered codon in [exn-5] specifies an isoleucine residue rather than the wild-type threonine residue. The corresponding position in subunit 2 sequences of all other organisms examined is conserved either as a threonine or a serine residue. Thus, we consider it likely that the mutation directly affecting the coding sequence of the polypeptide is responsible for the [exn-5] phenotype. Analysis of serially passaged heterokaryons constructed between wild-type and [exn-5] shows that both mutations segregate with the [exn-5] phenotype. Examination of mitochondrial translation products in [exn-5] revealed a deficiency of subunit 2, as well as the presence of a polypeptide that corresponds to a previously described precursor of subunit 1 that accumulates in a COXI mutant of N. crassa, [mi-3]. We propose possible relationships between [exn-5], [mi-3], and the nuclear su-1 [mi-3] allele, which suppresses both mutations.
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  • 40
    ISSN: 1432-0983
    Keywords: Mitochondrial plasmids ; Epichloë typhina (Acremonium typhinum) ; Grass endophyte ; Reverse transcriptase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Epichloë typhina is a clavicipitaceous ascomycete which systemically infects grasses, causes choke disease of host inflorescences, and is related to a group of mutualistic grass endophytes. Three plasmids of 7.5, 2.1 and 2.0 kilobase pairs were found in mitochondrial DNA preparations of an E. typhina isolate from perennial ryegrass (Lolium perenne). Results of nuclease digestion indicated that the plasmids, designated Et7.5L, Et2.1L, and Et2.0L, were linear, double-stranded DNAs with protein linked to their 5′-ends (plDNA). The plasmids shared little or no homology with each other, and were not integrated into the mitochondrial or nuclear genomes. No homologous plasmids were detected in isolates of E. typhina from other grass hosts, anamorphic endophytes, or other Clavicipitaceae. However, other plasmids were present in Balansia obtecta and Claviceps purpurea. A partial sequence of one of the E. typhina plasmids, Et2.0L, indicated an open reading frame when UGA was assumed to encode tryptophan. The inferred amino acid sequence had 24% indentity over 258 amino acids in two regions of the reverse transcriptase encoded by the circular Mauriceville and Varkud plasmids of Neurospora spp. The homologies included six segments conserved in RNA template-dependent DNA or RNA polymerases.
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  • 41
    ISSN: 1432-0983
    Keywords: Linear mitochondrial plasmid ; Nucleotide sequence ; Viral DNA-polymerase ; Terminal inverted repeat (TIR) ; Adenovirus ; Morchella conica
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary pMC3-2, one of two linear plasmids localised in the mitochondria of the ascomycete Morchella conica, was completely sequenced. It is 6044 bp in size, contains terminal inverted repeats of 713 and 710 bp length and two open reading frames, ORF1 and ORF2, spanning 2706 bp and 918 bp, respectively. ORF1 probably encodes a viral B-type DNA-polymerase. Concerning ORF2, no homology to any other published protein-or DNA-sequence could be detected. According to the structure of DNA-polymerases, linear plasmids can be grouped into two classes reflecting their localisation either in the cytoplasm or within the mitochondria. In general, the structure of plasmid pMC3-2, as well as of other linear plasmids from filamentous fungi, indicates a close relationship of these genetic elements to adenoviruses.
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  • 42
    ISSN: 1432-0983
    Keywords: Rice ; NADH dehydrogenase subunit 3 ; Mitochondrial DNA ; Ribosomal protein S12 ; tRNASer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nucleotide sequences of the tRNASer (trnS), pseudo-tRNA, NADH dehydrogenase subunit 3 (nad3), and ribosomal protein S12 (rps12) genes from rice mitochondrial DNA (mtDNA) were determined. Both trnS and nad3 were confirmed to be single copy genes by Southern blot analysis. The nad3 and rps12 genes were arranged in tandem, and the two were co-transcribed. The order of the above four genes in rice mtDNA differed from the linear order observed for the wheat and maize genes. In rice mitochondria, the trnS and pseudo-tRNA genes were found upstream of the cytochrome c oxidase subunit I gene, instead of the nad3 and rps12 genes as observed in maize and wheat. Additionally, while the rice nad3 and rps12 genes remain paired, they too are in a different sequence environment from the wheat and maize genes. The apparent split of the two pairs of genes indicates the occurrence of a mitochondrial intramolecular recombinational event. Another peculiarity is that the sequence upstream of the translational initiation codon of the rice nad3 gene is different from that of the wheat and maize versions. The ATG initiation codon of wheat and maize nad3 is replaced by TTG in the rice nad3. A subsequent deduction of the amino acid sequence, accompanied by a primer extension analysis, indicates that the predicted rice NAD3 protein has an additional 37 amino acid residues at its N-terminus compared to the wheat and maize NAD3 proteins. cDNA sequence analysis showed no introns or the occurrence of RNA editing at the newly replaced TTG codon.
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  • 43
    ISSN: 1432-0983
    Keywords: Podospora anserina ; ATP synthase subunit 9 ; Nucleotide sequence ; Nuclear localisation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nuclear gene coding for the mitochondrial subunit 9 of the F0F1-ATP synthase complex was isolated from a genomic library of Podospora anserina. Nucleotide sequencing revealed an open reading frame capable to code for 144 amino acids including an amino-terminal pre-sequence of 63 amino acid residues for mitochondrial import of the pre-proteolipid. The P. anserina proteolipid shows extensive sequence identity with the corresponding gene products of the related filamentous fungi Neurospora crassa, Aspergillus nidulans and Aspergillus niger. In contrast to the situation in Saccharomyces cerevisiae, N. crassa and A. nidulans, no sequence similarity of the ATP synthase subunit 9 gene to the mitochondrial genome of P. anserina could be detected. Thus, in P. anserina this gene appears to be exclusively encoded by the nuclear genome.
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  • 44
    ISSN: 1432-0983
    Keywords: Albino pollen plant ; Direct embryogenesis ; Plastid genome structure ; Plastid-related gene expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Southern analysis of DNA from four albino barley plants regenerated from microspores by direct embryogenesis revealed the presence of plastid genomes which had undergone deletion or alteration of specific restriction fragments (ΔptDNAs). In contrast, a fifth plant appeared to contain an intact plastid genome. All the albino plants studied contained reduced amounts of ptDNA, the most abundant restriction fragments being present at levels between 6% and 20% of those found in the leaves of green seedlings. Steady-state levels of transcripts from plastid and nuclear genes encoding plastid components were estimated by Northern analysis of RNA from albino plants. Transcripts from the plastid genes rbcL, psbD-psbC and the 16S and 23S rRNAs were undetectable or were present at greatly reduced levels in albino plants compared to those found in green leaves. Transcripts from the nuclear genes rbcS and cab, which encode chloroplast localised proteins, were also present at reduced levels in albino pollen plants. Levels of the nuclear encoded 25S rRNA, which is not a plastid component, were found to be identical in albino plants and green leaves suggesting that only the expression of plastid-related genes may be affected in albino plants. The general reduction of plastid-related transcripts was independent of the different patterns of ptDNA alteration seen in albino pollen plants.
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  • 45
    ISSN: 1432-0983
    Keywords: Codon usage ; Transcription unit ; Gene location ; RNA polymerase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A characteristic profile of the fluctuations of codon usage is observed in bacteriophages and mitochondria. By following the DNA in the direction of transcription, one moves slowly from a region where selective pressure favours codons ending with C to a region where the bias is in favour of codons ending with T; then, abruptly, one again enters a region of codons ending in C. The transcription end point takes place in the area of abrupt change in codon usage. By comparing Drosophila yakuba and mouse mitochondrial genomes, it is possible to show that the strategy of codon usage for a given gene depends on its location along the transcription unit and not on the encoded protein. The choice of codons ending in T or C allows large scale variations of DNA stability which could regulate the speed of propagation of the RNA polymerase.
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  • 46
    ISSN: 1432-0983
    Keywords: Rhizopus niveus ; Blasticidin S resistance gene ; Transformation ; Heterologous gene expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Rhizopus niveus has been transformed to blasticidin S resistance by vectors containing the bacterial blasticidin S resistance gene under the control of a Rhizopus promoter. Southern analysis of the total DNA from transformants indicated that the introduced DNA was rearranged, and that one of the transformants harbored extrachromosomal plasmids with rearranged DNA. Using this transformation system, the introduction of pUBSR101, a plasmid carrying the Escherichia coli lacZ gene fused to the promoter and the N-terminal region of the R. niveus aspartic proteinase-II (RNAP-II) gene, resulted in an increase of β-galactosidase activity in the cell extract, indicating expression of the lacZ fusion gene in R. niveus. This is the first report of a transformation system for filamentous fungi using the blasticidin S resistance gene as a dominant selectable marker.
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  • 47
    ISSN: 1432-0983
    Keywords: psaI ; Thylakoid membrane protein ; Zinc finger protein ; zfpA ; Propionyl-CoA carboxylase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nucleotide sequence of 3.2 kbp of pea chloroplast DNA located upstream from the petA gene for cytochrome f, and previously reported to contain the gene for a photosystem I polypeptide, has been determined. Three open reading frames of 587, 40 and 157 codons have been identified. Orf40 encodes a highly conserved, hydrophobic, membrane-spanning polypeptide, and is identified as the gene psaI for the 4 kDa subunit of photosystem I. Orf587 is an extended version of the gene zfpA previously identified as encoding a conserved putative zinc-finger protein. The product of orf587 shows extensive homology to an unidentified open reading frame cotranscribed with a gene for folate metabolism in Escherichia coli and local homology to a region of the β subunit of rat mitochondrial propionyl-CoA carboxylase. It is suggested that the product of orf587 is an enzyme of C1 metabolism and is unlikely to be a regulatory DNA-binding protein. Orf157 potentially encodes an unidentified basic protein, but the protein sequence is not conserved in other plants.
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  • 48
    ISSN: 1432-0983
    Keywords: Agaricus ; Mitochondria ; Plasmid ; RNA polymerase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Agaricus bisporus, the cultivated mushroom, contains a mitochondrial fragment (50H) which was previously demonstrated by Southern hybridization to have sequence similarity to an internal region of pEM, a linear mitochondrial plasmid of Agaricus bitorquis. The nucleotide sequence of 50H was determined and compared to the sequence of the corresponding pEM fragment. The region of sequence homology on pEM is contained within an open reading frame (ORF) that may encode an RNA polymerase, but 50H is neither an intact nor a complete copy of the ORF. pEM also contains an ORF with characteristics of genes for virus-encoded DNA polymerases. pEM appears to be very similar to other linear mitochondrial plasmids (in fungi and higher plants) reported to contain ORFs that may encode the same types of polymerases. The potential functionality of the pEM sequence suggests that it has diverged less than the mitochondrial fragment from a common ancestor.
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  • 49
    ISSN: 1432-1017
    Keywords: Maximum likelihood ; Fluorescence decay
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The usefulness of fluorescence techniques for the study of macromolecular structure and dynamics depends on the accuracy and sensitivity of the methods used for data analysis. Many methods for data analysis have been proposed and used, but little attention has been paid to the maximum likelihood method, generally known as the most powerful statistical method for parameter estimation. In this paper we study the properties and behavior of maximum likelihood estimates by using simulated fluorescence intensity decay data. We show that the maximum likelihood method provides generally more accurate estimates of lifetimes and fractions than does the standard least-squares approach especially when the lifetime ratios between individual components are small. Three novelties to the field of fluorescence decay analysis are also introduced and studied in this paper: a) discretization of the convolution integral based on the generalized integral mean value theorem: b) the likelihood ratio test as a tool to determine the number of exponential decay components in a given decay profile; and c) separability and detectability indices which provide measures on how accurately, a particular decay component can be detected. Based on the experience gained from this and from our previous study of the Padé-Laplace method, we make some recommendations on how the complex problem of deconvolution and parameter estimation of multiexponential functions might be approached in an experimental setting.
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  • 50
    ISSN: 1432-1017
    Keywords: Reverse micelle ; Percolation ; Biotechnology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract On addition of cytochrome c to a AOT reverse micellar solution, the percolation process usually observed at high temperatures and surfactant concentrations, occurs at room temperature. This is observed either at relatively high water content at a given cytochrome c concentration or at low content on increasing the cytochrome c concentration. On increasing the water content a phase transition is observed with two optically transparent phases. A similar phase transition is observed on solubilizing various enzymes. The temperature of the transition appears to be strongly dependent on the location of the macromolecule in the reserve micelle.
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  • 51
    ISSN: 1432-1017
    Keywords: Sodium channel ; Patch clamp ; Cerebellar ; granule cells ; Intracellular magnesium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The aim of this study was to determine from macroscopic current analysis how intracellular magnesium ions, Mg i 2+ , interfere with sodium channels of mammalian neurones. It is reported here that permeation across the sodium channel is voltage- and concentration-dependently reduced by Mg i 2+ . This results in a general reduction of sodium membrane conductance and an outward sodium peak current at large positive potentials. 30 mM Mg i 2+ leads to a negative shift of voltage dependence of sodium channel gating parameters, probably due to the surface potential change of the membrane. This shift alone is, however, insufficient to explain the reduction of outward sodium currents. The blockage by Mg i 2+ is decreased upon increasing intracellular or extracellular Na+ concentration, which suggests that Mg?' interferes with sodium permeation by competitively occupying sodium channels. Using a kinetic model to describe the sodium permeation, the dissociation constant (at zero membrane potential) of Mg i 2+ for the sodium channel has been calculated to be 8.65 ± 1.51 mM, with its binding site located at 0.26 ± 0.05 electrical distance from the inner membrane. This dissociation constant is smaller than that of Na i +, which is 83.76 ± 7.60 mM with its binding site located at 0.75 ± 0.23. The low dissociation constant of Mg i 2+ reflects its high affinity for the sodium channel.
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  • 52
    ISSN: 1432-1017
    Keywords: Skeletal muscle ; Potassium channel ; Patch clamp ; ATP ; Vanadate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The inside-out mode of the patch-clamp technique was used to study adenosine-5′-triphosphate (ATP)-sensitive K+ channels in mammalian skeletal muscle. Vanadate, applied to the cytoplasmic face of excised patches, was a potent activator of ATP-sensitive K+ channels. Divalent cations (Mg2+, Ca2+) were a prerequisite for the activating process. The maximal effect was achieved using 1 mM vanadate dissolved in Ringer, increasing the open-state probability about ninefold. The active 5 + redox form of vanadate which stimulates ATP-sensitive K+ channels is likely to be decavanadate V10O inf28 sup6− . ATP concentration-response curves have Hill coefficients near three in internal Na+-rich Ringer and between one and two in internal KCl solutions. Half maximal channel blockage was observed at ATP concentrations of 4 and 8 μM in Ringer and KCl solutions, respectively. Internal vanadate shifted the curves towards higher ATP concentrations without affecting their slopes. Thus 50% channel blockage occurred at 65 μM ATP in internal Ringer containing 0.5 mM vanadate. The results indicate that the affinity and stoichiometry of ATP binding to ATP-sensitive K+ channels are strongly modulated by internal cations and that the ATP sensitivity is weakened by vanadate.
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  • 53
    ISSN: 1432-1017
    Keywords: Superoxide dismutase ; NMR spectroscopy ; Metal substitution ; Superoxide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The activity profile of the CU2Zn2HSOD Ile-137 mutant has a pKa of 9.6, i. e. one unit lower than the wild type (WT). This property has allowed us to investigate the inactive high pH form of the enzyme before denaturation occurs. The electronic and EPR spectra do not change with the above pKa. The 1H NMR spectrum of the CU2CO2-analog reveals slight decreases in the hyperfine shifts of the protons of His-48 at high pH, which are consistent with a water molecule becoming closer to the copper ion, as detected through water 1H T 1 −1 NMR measurements. The affinity of azide at high pH is lower than at low pH, though still sizeable. The WT follows the same pattern up to pH ≅ pKa. It appears that the drop in activity is not related to any major change involving the metal coordination sphere, but is related to changes in the electrostatic potential due to the deprotonation process.
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  • 54
    ISSN: 1432-1017
    Keywords: Protein dynamics ; Anisotropy ; Fluorescence ; Proteins ; Frequency-domain fluorescence ; Quenching ; Fluorescence quenching
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract We used harmonic-content frequency-domain fluorometry to determine the anisotropy decays of a variety of single tryptophan peptides and proteins. Resolution of the rapid and complex anisotropy decays was enhanced by global analysis of the data measured in the presence of quenching by either oxygen or acrylamide. For each protein, and for each quencher, data were obtained at four to six quencher concentrations, and the data analyzed globally to recover the anisotropy decay. The decrease in decay times produced by quenching allows measurements to an upper frequency limit of 2 GHz. The chosen proteins provided a range of exposures of the tryptophan residues to the aqueous phase, these being ACTH, monellin, Staphylococcus nuclease and ribonuclease T 1, in order of decreasing exposure. Examination of indole and several small peptides demonstrates the resolution limitations of the measurements; a correlation time of 12 ps was measured for indole in methanol at 40°C. Comparison of the anisotropy decays of gly-trp-gly with leu-trp-leu revealed stearic effects of the larger leucine side chains on the indole ring. The anisotropy decay of gly-trp-gly revealed a 40 ps component for the indole side chain, which was resolved from the overall 150 ps correlation time of the tripeptide. Only the longer correlation time was observed for leu-trp-leu. With the exception of ribonuclease T 1, each of the proteins displayed a subnanosecond component in the anisotropy decay which we assign to independent motions of the tryptophan residues. For example, Staphylococcus nuclease and monellin displayed segmental tryptophan motions with correlation times of 80 and 275 ps, respectively. The amplitudes of the rapid components increased with increasing exposure to the aqueous phase. These highly resolved anisotropy decays for proteins of known structure are suitable for comparison with molecular dynamic simulations.
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  • 55
    ISSN: 1432-1017
    Keywords: Actin ; Solid-state NMR spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Solid-state nuclear magnetic resonance spectroscopy was used to study the motion of 2H and 19F probes attached to the skeletal muscle actin residues Cys-10, Lys-61 and Cys-374. The probe resonances were observed in dried and hydrated G-actin, F-actin and F-actin-myosin subfragment-1 complexes. Restricted motion was exhibited by 19F probes attached to Cys-10 and Cys-374 on actin. The dynamics of probes attached to dry cysteine powder or F-actin were very similar and the binding of myosin had little effect indicating that the local probe environment imposes the major influence on motion in the solid state. Correlation times determined for the solid state probes indicated that they were undergoing some rapid internal motion in both G-actin and F-actin such as domain twisting. The probe size influenced the motion in G-actin and appeared to sense monomer rotation but not in F-actin where segmental mobility and intramonomer co-ordination appeared to dominate.
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  • 56
    ISSN: 1432-1017
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
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  • 57
    ISSN: 1432-1017
    Keywords: Lipid-protein interactions ; Phase transition ; Lipid bilayer ; Hydropobic thickness ; Protein aggregation ; Monte Carlo simulation ; Mean-field theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Monte Carlo simulations and mean-field calculations have been applied to a statistical mechanical lattice model of lipid-protein interactions in membranes in order to investigate the phase equilibria as well as the state of aggregation of small integral membrane proteins in dipalmitoyl phosphatidylcholine bilayers. The model, which provides a detailed description of the pure lipid bilayer phase transition, incorporates hydrophobic matching between the lipid and protein hydrophobic thicknesses as a major contribution to the lipid-protein interactions. The model is analyzed in the regime of low protein concentration. It is found that a large mismatch between the lipid and protein hydrophobic thicknesses does not guarantee protein aggregation even though it strongly affects the phase behaviour. This result is consistent with experimental work (Lewis and Engelman 1983) considering the effect of lipid acyl-chain length on the planar organization of bacteriorhodopsin in fluid phospholipid bilayers. The model calculations predict that the lipid-mediated formation of protein aggregates in the membrane plane is mainly controlled by the strength of the direct lipid-protein hydrophobic attractive interaction but that direct protein-protein interactions are needed to induce substantial aggregation.
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  • 58
    ISSN: 1432-1017
    Keywords: Multicellular tumor spheroids ; Concentration distribution ; Parameter dependence ; Mathematical model ; Nomogram ; Metabolite diffusion ; Metabolite consumption/production
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The distribution of oxygen, nutrients and metabolic wastes in multicellular tumor spheroids and its dependence on the parameters characterizing the spheroid (i.e., spheroid geometry, diffusivity, and consumption/ production rates of biological substances) have been investigated by a theoretical analysis: 1. Parameter dependence is qualitatively demonstrated and visualized. 2. Reduction of the number of variables by specific coordinate transformations made it possible to generate nomograms from which concentration distributions for any choice of parameter values may easily be obtained. In particular, these nomograms may also be used for estimating concentration profiles of metabolic waste products, e.g. of lactate, which are expected to accumulate in the tumor spheroids. 3. An additional set of nomograms is given which is more convenient for determining time courses of these concentrations during spheroid growth. 4. A quantitative sensitivity analysis of parameter dependencies is performed to identify those parameters upon which a concentration of interest depends most critically in a given experimental situation.
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  • 59
    ISSN: 1432-1017
    Keywords: Membrane potential ; Fluorescence ; diS-C3(5) ; Synchronous excitation spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The fluorescence of the voltage sensitive dye, diS-C3-(5), has been analyzed by means of synchronous excitation spectroscopy. Using this rather rare fluorescence technique we have been able to distinguish between the slightly shifted spectra of diS-C3-(5) fluorescence from cells and from the supernatant. It has been found that diS-C3-(5) fluorescence in the supernatant can be selectively monitored at λexc = 630 nm and λem= 650 nm, while the cell associated fluorescence can be observed at λexc= 690 nm and λem = 710 nm. A modified theory for the diSC3-(5) fluorescence response to the membrane potential is presented, according to which a linear relationship exists between the logarithmic increment of the dye fluorescence intensity in the supernatant, In I/I°, and the underlying change in the plasma membrane potential, Δψp=ψp-ψ°p. The theory has been tested on human myeloid leukemia cells (line ML-1) in which membrane potential changes were induced by valinomycin clamping in various K+ gradients. It has been demonstrated that the membrane potential change, Δψp,can be measured on an absolute scale.
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  • 60
    ISSN: 1432-1017
    Keywords: Transmembrane pH difference ; Fluorescent probes ; Bacterial chromatophores ; Adsorption isotherms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract In chromatophores from photosynthetic bacteria the interaction of the fluorescent monoamine, 9-amino, 6-chloro, 2-methoxyacridine (ACMA), with the membrane is evaluated and described by an S-shaped adsorption isotherm. This phenomenon is hysteretic, as indicated by the difference between the adsorption and desorption branches of the binding isotherm. Maximal saturation of adsorption is reached at one ACMA per one to four lipid molecules, indicating that the probe binds in its neutral form. Adsorption of the probe on the membrane causes a large quenching of its fluorescence, which is explaind as being due to hypochromic effects following stacking and aggregation in a medium of low dielectric constant. A further quenching of fluorescence is brought about by imposing artificially induced transmembrane ΔpH's. This latter phenomenon titrates in at increasing ΔpH values and approaches saturation when ΔpH is ≧2. The dependence of ΔpH on the observed quenching of fluorescence is predicted by considering a model based on the equilibrium distribution of the amine between two phases at different pH's, in which adsorption of the probe on the membrane is used to evaluate its free concentration in the inner and outer compartments of the chromatophore vesicle. It is proposed that the equation thus obtained should be used to measure ΔpH from the quenching of ACMA fluorescence.
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  • 61
    ISSN: 1432-1017
    Keywords: Photosynthesis ; Chromatophore ; Gramicidin ; Electrochromism ; Size analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Chromatophores of Rhodobacter sphaeroides were excited with light flashes to generate a transmembrane electrical potential difference. The electric relaxation was measured by electrochromic absorption changes as a function of added gramicidin. At low gramicidin/bacteriochlorophyll (BChl) molar ratios the decay of the electrochromic absorption changes showed a biphasic behaviour, with a fast phase relaxing at some μs, and a slow phase relaxing at more than 100 ms. This was attributable to a mixture of vesicles containing gramicidin dimers with others containing none. The concentration dependence of this effect was linear. This implied full dimerization of gramicidin. The data were interpreted to yield an average bacteriochlorophyll content per chromatophore of 770(±150) and the conductance of a single gramicidin dimer in the chromatophore membrane of 15(±4) pS (in about 115 mM KCl).
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